| Item Type | Software |
|---|---|
| Programmer | Martin Morgan |
| Programmer | Marcel Ramos |
| Date | 2025 |
| URL | https://CRAN.R-project.org/package=BiocManager |
| Extra | DOI: 10.32614/CRAN.package.BiocManager |
| Version | 1.30.26 |
| Date Added | 6/25/2025, 11:34:24 AM |
| Modified | 6/25/2025, 11:45:37 AM |
R package version 1.30.26
| Item Type | Journal Article |
|---|---|
| Author | John H. Morris |
| Author | Leonard Apeltsin |
| Author | Aaron M. Newman |
| Author | Jan Baumbach |
| Author | Tobias Wittkop |
| Author | Gang Su |
| Author | Gary D. Bader |
| Author | Thomas E. Ferrin |
| Abstract | BACKGROUND: In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL. RESULTS: Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. CONCLUSIONS: The Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. clusterMaker is available via the Cytoscape plugin manager. |
| Date | 2011-11-09 |
| Language | eng |
| Short Title | clusterMaker |
| Library Catalog | PubMed |
| Extra | PMID: 22070249 PMCID: PMC3262844 |
| Volume | 12 |
| Pages | 436 |
| Publication | BMC bioinformatics |
| DOI | 10.1186/1471-2105-12-436 |
| Journal Abbr | BMC Bioinformatics |
| ISSN | 1471-2105 |
| Date Added | 6/29/2025, 11:56:34 AM |
| Modified | 6/29/2025, 11:56:34 AM |
| Item Type | Journal Article |
|---|---|
| Author | Yassen Assenov |
| Author | Fidel Ramírez |
| Author | Sven-Eric Schelhorn |
| Author | Thomas Lengauer |
| Author | Mario Albrecht |
| Abstract | Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path length, and the distributions of node degrees, neighborhood connectivities, average clustering coefficients, and shortest path lengths. NetworkAnalyzer can be applied to both directed and undirected networks and also contains extra functionality to construct the intersection or union of two networks. It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user. AVAILABILITY: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org |
| Date | 2008-01-15 |
| Language | eng |
| Library Catalog | PubMed |
| Extra | PMID: 18006545 |
| Volume | 24 |
| Pages | 282-284 |
| Publication | Bioinformatics (Oxford, England) |
| DOI | 10.1093/bioinformatics/btm554 |
| Issue | 2 |
| Journal Abbr | Bioinformatics |
| ISSN | 1367-4811 |
| Date Added | 6/29/2025, 11:56:21 AM |
| Modified | 6/29/2025, 11:56:21 AM |
| Item Type | Journal Article |
|---|---|
| Author | Martina Kutmon |
| Author | Friederike Ehrhart |
| Author | Egon L. Willighagen |
| Author | Chris T. Evelo |
| Author | Susan L. Coort |
| Abstract | Here, we present an update of the open-source CyTargetLinker app for Cytoscape ( http://apps.cytoscape.org/apps/cytargetlinker) that introduces new automation features. CyTargetLinker provides a simple interface to extend networks with links to relevant data and/or knowledge extracted from so-called linksets. The linksets are provided on the CyTargetLinker website ( https://cytargetlinker.github.io/) or can be custom-made for specific use cases. The new automation feature enables users to programmatically execute the app's functionality in Cytoscape (command line tool) and with external tools (e.g. R, Jupyter, Python, etc). This allows users to share their analysis workflows and therefore increase repeatability and reproducibility. Three use cases demonstrate automated workflows, combinations with other Cytoscape apps and core Cytoscape functionality. We first extend a protein-protein interaction network created with the stringApp, with compound-target interactions and disease-gene annotations. In the second use case, we created a workflow to load differentially expressed genes from an experimental dataset and extend it with gene-pathway associations. Lastly, we chose an example outside the biological domain and used CyTargetLinker to create an author-article-journal network for the five authors of this manuscript using a two-step extension mechanism. With 400 downloads per month in the last year and nearly 20,000 downloads in total, CyTargetLinker shows the adoption and relevance of the app in the field of network biology. In August 2019, the original publication was cited in 83 articles demonstrating the applicability in biomedical research. |
| Date | 2018 |
| Language | eng |
| Short Title | CyTargetLinker app update |
| Library Catalog | PubMed |
| Extra | PMID: 31489175 PMCID: PMC6707396 |
| Volume | 7 |
| Pages | ELIXIR-743 |
| Publication | F1000Research |
| DOI | 10.12688/f1000research.14613.2 |
| Journal Abbr | F1000Res |
| ISSN | 2046-1402 |
| Date Added | 6/29/2025, 11:56:08 AM |
| Modified | 6/29/2025, 11:56:08 AM |
| Item Type | Journal Article |
|---|---|
| Author | Nadezhda T. Doncheva |
| Author | John H. Morris |
| Author | Jan Gorodkin |
| Author | Lars J. Jensen |
| Abstract | Protein networks have become a popular tool for analyzing and visualizing the often long lists of proteins or genes obtained from proteomics and other high-throughput technologies. One of the most popular sources of such networks is the STRING database, which provides protein networks for more than 2000 organisms, including both physical interactions from experimental data and functional associations from curated pathways, automatic text mining, and prediction methods. However, its web interface is mainly intended for inspection of small networks and their underlying evidence. The Cytoscape software, on the other hand, is much better suited for working with large networks and offers greater flexibility in terms of network analysis, import, and visualization of additional data. To include both resources in the same workflow, we created stringApp, a Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains the appearance and many of the features of STRING, and integrates data from associated databases. Here, we introduce many of the stringApp features and show how they can be used to carry out complex network analysis and visualization tasks on a typical proteomics data set, all through the Cytoscape user interface. stringApp is freely available from the Cytoscape app store: http://apps.cytoscape.org/apps/stringapp . |
| Date | 2019-02-01 |
| Language | eng |
| Short Title | Cytoscape StringApp |
| Library Catalog | PubMed |
| Extra | PMID: 30450911 PMCID: PMC6800166 |
| Volume | 18 |
| Pages | 623-632 |
| Publication | Journal of Proteome Research |
| DOI | 10.1021/acs.jproteome.8b00702 |
| Issue | 2 |
| Journal Abbr | J Proteome Res |
| ISSN | 1535-3907 |
| Date Added | 6/29/2025, 11:56:50 AM |
| Modified | 6/29/2025, 11:56:50 AM |
| Item Type | Journal Article |
|---|---|
| Author | Paul Shannon |
| Author | Andrew Markiel |
| Author | Owen Ozier |
| Author | Nitin S. Baliga |
| Author | Jonathan T. Wang |
| Author | Daniel Ramage |
| Author | Nada Amin |
| Author | Benno Schwikowski |
| Author | Trey Ideker |
| Abstract | Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models. |
| Date | 2003-11 |
| Language | eng |
| Short Title | Cytoscape |
| Library Catalog | PubMed |
| Extra | PMID: 14597658 PMCID: PMC403769 |
| Volume | 13 |
| Pages | 2498-2504 |
| Publication | Genome Research |
| DOI | 10.1101/gr.1239303 |
| Issue | 11 |
| Journal Abbr | Genome Res |
| ISSN | 1088-9051 |
| Date Added | 6/29/2025, 11:55:53 AM |
| Modified | 6/29/2025, 9:33:43 PM |
| Item Type | Software |
|---|---|
| Programmer | Hadley Wickham |
| Programmer | Romain François |
| Programmer | Lionel Henry |
| Programmer | Kirill Müller |
| Programmer | Davis Vaughan |
| Date | 2023 |
| URL | https://CRAN.R-project.org/package=dplyr |
| Extra | DOI: 10.32614/CRAN.package.dplyr |
| Version | 1.1.4 |
| Date Added | 6/25/2025, 11:38:21 AM |
| Modified | 6/25/2025, 11:46:28 AM |
R package version 1.1.4
| Item Type | Journal Article |
|---|---|
| Author | John H. Morris |
| Author | Allan Kuchinsky |
| Author | Thomas E. Ferrin |
| Author | Alexander R. Pico |
| Abstract | enhancedGraphics ( http://apps.cytoscape.org/apps/enhancedGraphics) is a Cytoscape app that implements a series of enhanced charts and graphics that may be added to Cytoscape nodes. It enables users and other app developers to create pie, line, bar, and circle plots that are driven by columns in the Cytoscape Node Table. Charts are drawn using vector graphics to allow full-resolution scaling. |
| Date | 2014 |
| Language | eng |
| Short Title | enhancedGraphics |
| Library Catalog | PubMed |
| Extra | PMID: 25285206 PMCID: PMC4176421 |
| Volume | 3 |
| Pages | 147 |
| Publication | F1000Research |
| DOI | 10.12688/f1000research.4460.1 |
| Journal Abbr | F1000Res |
| ISSN | 2046-1402 |
| Date Added | 6/29/2025, 11:56:42 AM |
| Modified | 6/29/2025, 11:56:42 AM |
| Item Type | Software |
|---|---|
| Programmer | Kevin Blighe |
| Programmer | Sharmila Rana |
| Programmer | Myles Lewis |
| Date | 2025 |
| URL | https://bioconductor.org/packages/EnhancedVolcano |
| Extra | DOI: 10.18129/B9.bioc.EnhancedVolcano |
| Version | 1.26.0 |
| Date Added | 6/25/2025, 11:38:42 AM |
| Modified | 6/25/2025, 11:46:14 AM |
R package version 1.26.0
| Item Type | Software |
|---|---|
| Programmer | Guangchuang Yu |
| Date | 2025 |
| URL | https://bioconductor.org/packages/enrichplot |
| Extra | DOI: 10.18129/B9.bioc.enrichplot |
| Version | 1.28.2 |
| Date Added | 6/25/2025, 11:40:53 AM |
| Modified | 6/25/2025, 11:45:18 AM |
R package version 1.28.2
| Item Type | Journal Article |
|---|---|
| Author | Uku Raudvere |
| Author | Liis Kolberg |
| Author | Ivan Kuzmin |
| Author | Tambet Arak |
| Author | Priit Adler |
| Author | Hedi Peterson |
| Author | Jaak Vilo |
| Abstract | Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler. |
| Date | 2019-07-02 |
| Language | eng |
| Short Title | g |
| Library Catalog | PubMed |
| Extra | PMID: 31066453 PMCID: PMC6602461 |
| Volume | 47 |
| Pages | W191-W198 |
| Publication | Nucleic Acids Research |
| DOI | 10.1093/nar/gkz369 |
| Issue | W1 |
| Journal Abbr | Nucleic Acids Res |
| ISSN | 1362-4962 |
| Date Added | 6/29/2025, 11:56:14 AM |
| Modified | 6/29/2025, 11:56:14 AM |
| Item Type | Software |
|---|---|
| Programmer | Igor Dolgalev |
| Date | 2025 |
| URL | https://CRAN.R-project.org/package=msigdbr |
| Extra | DOI: 10.32614/CRAN.package.msigdbr |
| Version | 24.1.0 |
| Date Added | 6/25/2025, 11:41:52 AM |
| Modified | 6/25/2025, 11:45:58 AM |
R package version 24.1.0
| Item Type | Software |
|---|---|
| Programmer | Marc Carlson |
| Date | 2025 |
| Library Catalog | DOI.org (Datacite) |
| URL | https://bioconductor.org/packages/org.Hs.eg.db |
| Accessed | 6/25/2025, 11:35:12 AM |
| Extra | DOI: 10.18129/B9.BIOC.ORG.HS.EG.DB |
| Version | 3.21.0 |
| Company | Bioconductor |
| Date Added | 6/25/2025, 11:35:12 AM |
| Modified | 6/25/2025, 11:36:56 AM |
| Item Type | Software |
|---|---|
| Programmer | Mar Roca Cugat |
| Programmer | Ina De Rijk |
| Programmer | Ivan Sapsai |
| Programmer | Daniela Sara Mirensky Roffe |
| Date | 2025-06-29T10:01:16Z |
| Library Catalog | GitHub |
| URL | doi.org/10.5281/zenodo.15767006 |
| Accessed | 6/23/2025, 2:24:32 PM |
| Rights | AGPL-3.0 |
| Extra | original-date: 2025-06-22T23:25:44Z |
| Prog. Language | R |
| Date Added | 6/23/2025, 2:24:32 PM |
| Modified | 6/29/2025, 12:26:46 PM |
| Item Type | Software |
|---|---|
| Programmer | R Core Team |
| Date | 2025 |
| URL | https://www.R-project.org/ |
| Place | Vienna, Austria |
| Version | 4.5.1 |
| Company | R Foundation for Statistical Computing |
| Date Added | 6/25/2025, 11:32:55 AM |
| Modified | 6/25/2025, 11:35:54 AM |
| Item Type | Software |
|---|---|
| Programmer | Erich Neuwirth |
| Date | 2022 |
| URL | https://CRAN.R-project.org/package=RColorBrewer |
| Extra | DOI: 10.32614/CRAN.package.RColorBrewer |
| Version | 1.1-3 |
| Date Added | 6/25/2025, 11:42:07 AM |
| Modified | 6/25/2025, 11:46:35 AM |
R package version 1.1-3
| Item Type | Journal Article |
|---|---|
| Author | Gustavsen |
| Author | Julia A |
| Author | Pai |
| Author | Shraddha |
| Author | Isserlin |
| Author | Ruth |
| Author | Demchak |
| Author | Barry |
| Author | Pico |
| Author | Alexander R |
| Date | 2019 |
| Publication | F1000Research |
| DOI | 10.12688/f1000research.20887.3 |
| Date Added | 6/25/2025, 11:41:22 AM |
| Modified | 6/25/2025, 11:41:22 AM |
| Item Type | Software |
|---|---|
| Programmer | Hadley Wickham |
| Programmer | Jim Hester |
| Programmer | Jennifer Bryan |
| Date | 2024 |
| URL | https://CRAN.R-project.org/package=readr |
| Extra | DOI: 10.32614/CRAN.package.readr |
| Version | 2.1.5 |
| Date Added | 6/25/2025, 11:43:44 AM |
| Modified | 6/25/2025, 11:46:21 AM |
R package version 2.1.5
| Item Type | Software |
|---|---|
| Programmer | Hadley Wickham |
| Programmer | Jennifer Bryan |
| Date | 2025 |
| URL | https://CRAN.R-project.org/package=readxl |
| Extra | DOI: 10.32614/CRAN.package.readxl |
| Version | 1.4.5 |
| Date Added | 6/25/2025, 11:39:03 AM |
| Modified | 6/25/2025, 11:45:24 AM |
R package version 1.4.5
| Item Type | Software |
|---|---|
| Programmer | Kasper Daniel Hansen |
| Programmer | Jeff Gentry |
| Programmer | Li Long |
| Programmer | Robert Gentleman |
| Programmer | Seth Falcon |
| Programmer | Florian Hahne |
| Programmer | Deepayan Sarkar |
| Date | 2025 |
| URL | https://bioconductor.org/packages/Rgraphviz |
| Extra | DOI: 10.18129/B9.bioc.Rgraphviz |
| Version | 2.52.0 |
| Date Added | 6/25/2025, 11:41:06 AM |
| Modified | 6/25/2025, 11:45:46 AM |
R package version 2.52.0
| Item Type | Software |
|---|---|
| Programmer | Posit team |
| Date | 2025 |
| URL | http://www.posit.co/ |
| Place | Boston, MA |
| Version | 2025.5.1.513 |
| Company | Posit Software, PBC |
| Date Added | 6/25/2025, 11:32:18 AM |
| Modified | 6/25/2025, 11:35:50 AM |
| Item Type | Journal Article |
|---|---|
| Author | Shuangbin Xu |
| Author | Erqiang Hu |
| Author | Yantong Cai |
| Author | Zijing Xie |
| Author | Xiao Luo |
| Author | Li Zhan |
| Author | Wenli Tang |
| Author | Qianwen Wang |
| Author | Bingdong Liu |
| Author | Rui Wang |
| Author | Wenqin Xie |
| Author | Tianzhi Wu |
| Author | Liwei Xie |
| Author | Guangchuang Yu |
| Date | 2024-11 |
| URL | https://www.nature.com/articles/s41596-024-01020-z |
| Volume | 19 |
| Pages | 3292-3320 |
| Publication | Nature Protocols |
| DOI | 10.1038/s41596-024-01020-z |
| Issue | 11 |
| Date Added | 6/25/2025, 11:40:33 AM |
| Modified | 6/25/2025, 11:40:33 AM |
| Item Type | Journal Article |
|---|---|
| Author | Martina Kutmon |
| Author | Samad Lotia |
| Author | Chris T. Evelo |
| Author | Alexander R. Pico |
| Abstract | In this paper we present the open-source WikiPathways app for Cytoscape ( http://apps.cytoscape.org/apps/wikipathways) that can be used to import biological pathways for data visualization and network analysis. WikiPathways is an open, collaborative biological pathway database that provides fully annotated pathway diagrams for manual download or through web services. The WikiPathways app allows users to load pathways in two different views: as an annotated pathway ideal for data visualization and as a simple network to perform computational analysis. An example pathway and dataset are used to demonstrate the functionality of the WikiPathways app and how they can be combined and used together with other apps. More than 3000 downloads in the first 12 months following its release in August 2013 highlight the importance and adoption of the app in the network biology field. |
| Date | 2014 |
| Language | eng |
| Short Title | WikiPathways App for Cytoscape |
| Library Catalog | PubMed |
| Extra | PMID: 25254103 PMCID: PMC4168754 |
| Volume | 3 |
| Pages | 152 |
| Publication | F1000Research |
| DOI | 10.12688/f1000research.4254.2 |
| Journal Abbr | F1000Res |
| ISSN | 2046-1402 |
| Date Added | 6/29/2025, 11:56:28 AM |
| Modified | 6/29/2025, 11:56:28 AM |
| Item Type | Journal Article |
|---|---|
| Author | Denise N. Slenter |
| Author | Martina Kutmon |
| Author | Kristina Hanspers |
| Author | Anders Riutta |
| Author | Jacob Windsor |
| Author | Nuno Nunes |
| Author | Jonathan Mélius |
| Author | Elisa Cirillo |
| Author | Susan L. Coort |
| Author | Daniela Digles |
| Author | Friederike Ehrhart |
| Author | Pieter Giesbertz |
| Author | Marianthi Kalafati |
| Author | Marvin Martens |
| Author | Ryan Miller |
| Author | Kozo Nishida |
| Author | Linda Rieswijk |
| Author | Andra Waagmeester |
| Author | Lars M. T. Eijssen |
| Author | Chris T. Evelo |
| Author | Alexander R. Pico |
| Author | Egon L. Willighagen |
| Abstract | WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. |
| Date | 2018-01-04 |
| Language | eng |
| Short Title | WikiPathways |
| Library Catalog | PubMed |
| Extra | PMID: 29136241 PMCID: PMC5753270 |
| Volume | 46 |
| Pages | D661-D667 |
| Publication | Nucleic Acids Research |
| DOI | 10.1093/nar/gkx1064 |
| Issue | D1 |
| Journal Abbr | Nucleic Acids Res |
| ISSN | 1362-4962 |
| Date Added | 6/25/2025, 11:44:18 AM |
| Modified | 6/25/2025, 11:44:18 AM |